AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irhaS_ecoli_opreg_300.orf -g0.5 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 rhaD 300 rhamnulose-phosphate aldolase #2 rhaB_rhaS 287 rhaB: rhamnulokinase, rhaS: positive regulator for rhaBAD operon #3 rhaT 284 rhamnose transport Motif number 1 CGACGCTGTCGCGTCTTATCAGGC 1 1 0 GGCTATCGGC 0.999405 -300 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 19 1 GGCCATCGGC 0.999547 -282 TAAGGCACTTGTGCCGCATCCGGCAATCAATGCC 1 40 0 GGCCATCGGC 0.999548 -261 TGCGGCACAAGTGCCTTATCCGGCCTACAGGTCG 1 56 1 GGCTATCGGC 0.999446 -245 CGACGCTGTCGCGTCTTATCAGGCCTACAACTGT 1 93 0 GGCTATCGGC 0.999405 -208 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 111 1 GGCCATCGGC 0.999547 -190 ATAAGCGACTTGTGCGCATCCGGCAATCAATGCC 1 132 0 TTCCATCGGC 0.957384 -169 ATGCGCACAAGTCGCTTATCAGGCCTACAGGTCG 1 147 1 GCCTATCGGC 0.998395 -154 CGACGCTGTCGCGTCTTATCAGGCCTACAACTAT 1 184 0 GGCTATCGGC 0.999405 -117 AGACGCGACAGCGTCGCATCAGGCATTGATTGCC 1 202 1 GGCCATCGGC 0.999547 -99 ATGCGCGCGAGCGCCTTATCCGGCCTACGGGTCG 1 240 1 GGCTATCGGC 0.999405 -61 CGGCCTACGGGTCGTGCATCCGACAACACCGAAT 1 260 1 GCTCATCGAC 0.877088 -41 GGTGATTTGCTTCACATCTCGGGCATTTTCCTGC 3 135 0 TCCTCTCGGC 0.965508 -150 TTTTCGTCGCGTCACATCTCCGACGAGATGAGTG 3 244 0 GCCTCTCGAC 0.964848 -41 * * * **** *** Masking position 9 Map Score: 63.4727 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 163 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 GCCTGATAAGACGCGACAGCGTCGCATCAGG 1 10 1 GACGCGAGCG 0.992895 -291 GTCGCATCAGGCATTGATTGCCGGATGCGGCA 1 31 1 GCATTGAGCC 0.917995 -270 AACTGTTGCCGACCTGTAGGCCGGATAAGGCA 1 67 0 GACCTGTGCC 0.991957 -234 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 1 102 1 GACGCGAGCG 0.992895 -199 GTCGCATCAGGCATTGATTGCCGGATGCGCAC 1 123 1 GCATTGAGCC 0.917995 -178 CCTGATAAGCGACTTGTGCGCATCCGGCAATC 1 138 0 GACTTGTGCA 0.922032 -163 AACTATTGCCGACCTGTAGGCCTGATAAGCGA 1 158 0 GACCTGTGCC 0.991957 -143 GGCCTGATAAGACGCGACAGCGTCGCATCAGG 1 193 1 GACGCGAGCG 0.992895 -108 GGCATTGATTGCCGTGGATGCGCGCGAGCGCC 1 223 1 GCCGTGGGCG 0.992889 -78 TCGGATGCACGACCCGTAGGCCGGATAAGGCG 1 251 0 GACCCGTGCC 0.991169 -50 TTACTATTTCGCCGTGTTGACGACATCAGGAG 2 17 0 GCCGTGTACG 0.937537 -271 CGTTCATCTTTCCCTGGTTGCCAATGGCCCAT 2 188 1 TCCCTGGGCC 0.872802 -100 GATTGTTAATGCCGCGTAAGCAGTTGGTTCAT 3 38 1 GCCGCGTGCA 0.983916 -247 CCCACTTAATGCCGTGATTGCCAGTAAATCGA 3 167 1 GCCGTGAGCC 0.997081 -118 ******* *** Masking position 11 Map Score: 32.3378 Number of sites scoring better than the average of aligned sites = 1611 Number in coding regions = 1369 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 3 GCGTCGCATCAGGCATTGATTGCCGGATGCGG 1 29 1 AGGCATTGAG 0.978377 -272 GCCTACAGGTCGGCAACAGTTGTAGGCCTGAT 1 78 1 CGGCAACAGG 0.987338 -223 GCGTCGCATCAGGCATTGATTGCCGGATGCGC 1 121 1 AGGCATTGAG 0.978377 -180 GCCTACAGGTCGGCAATAGTTGTAGGCCTGAT 1 169 1 CGGCAATAGG 0.991673 -132 GCGTCGCATCAGGCATTGATTGCCGTGGATGC 1 212 1 AGGCATTGAG 0.978377 -89 GCCGTGTTGACGACATCAGGAGGCCAGT 2 7 0 CGACATCAGG 0.953312 -281 ATCGGCCGCCCGACAATACTGGAGATGAAT 3 9 0 CGACAATACG 0.845177 -276 ACTGCTTACGCGGCATTAACAATCGGCCGCCC 3 30 0 CGGCATTAAA 0.967837 -255 ACGAAAAGTACGGCATTGATAATCATTTTCAA 3 89 0 CGGCATTGAA 0.965685 -196 CTGGCAATCACGGCATTAAGTGGGTGATTTGC 3 159 0 CGGCATTAAG 0.994906 -126 TCGACAACGGCGGCAACAGGCGAAAGGTTAAT 3 195 1 CGGCAACAGG 0.987152 -90 ********* * Masking position 5 Map Score: 20.9115 Number of sites scoring better than the average of aligned sites = 1358 Number in coding regions = 1265 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 TGATGCGACGCTGTCGCGTCTTATCAGGC 1 10 0 CTGTCGCGTC 0.995757 -291 CAATCAATGCCTGATGCGACGCTGTCGCGT 1 21 0 CTGATGCGAC 0.978091 -280 CCTTATCCGGCCTACAGGTCGGCAACAGTT 1 69 1 CCTACAGGTC 0.89138 -232 TGATGCGACGCTGTCGCGTCTTATCAGGCC 1 102 0 CTGTCGCGTC 0.995757 -199 CAATCAATGCCTGATGCGACGCTGTCGCGT 1 113 0 CTGATGCGAC 0.978091 -188 GCTTATCAGGCCTACAGGTCGGCAATAGTT 1 160 1 CCTACAGGTC 0.89138 -141 TGATGCGACGCTGTCGCGTCTTATCAGGCC 1 193 0 CTGTCGCGTC 0.995757 -108 CAATCAATGCCTGATGCGACGCTGTCGCGT 1 204 0 CTGATGCGAC 0.978091 -97 CCTTATCCGGCCTACGGGTCGTGCATCCGA 1 253 1 CCTACGGGTC 0.981573 -48 GAACCAACTGCTTACGCGGCATTAACAATC 3 38 0 CTTACGCGGC 0.9749 -247 TCATCATTTTTCGTCGCGTCACATCTCCGA 3 255 0 TCGTCGCGTC 0.945334 -30 ********** Masking position 10 Map Score: 24.7357 Number of sites scoring better than the average of aligned sites = 1438 Number in coding regions = 1210 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 GTTGCCGACCTGTAGGCCGGATAAGGCACT 1 65 0 TGTAGGCCGG 0.997038 -236 CGGCAACAGTTGTAGGCCTGATAAGACGCG 1 88 1 TGTAGGCCTG 0.997555 -213 ATTGCCGACCTGTAGGCCTGATAAGCGACT 1 156 0 TGTAGGCCTG 0.997555 -145 CGGCAATAGTTGTAGGCCTGATAAGACGCG 1 179 1 TGTAGGCCTG 0.997555 -122 ATGCACGACCCGTAGGCCGGATAAGGCGCT 1 249 0 CGTAGGCCGG 0.987444 -52 GTTCTGTGTTCCTGTAAATTCGGT 1 287 0 TGTGTTCCTG 0.936057 -14 TTTGCTGAATTGTGGTGATGTGATGCTCAC 2 143 0 TGTGGTGATG 0.796517 -145 AATGTGATCCTGCTGAATTTCA 2 276 0 TGTGATCCTG 0.936057 -12 TCTCCAGTATTGTCGGGCGGCCGATTGTTA 3 16 1 TGTCGGGCGG 0.974017 -269 ********** Masking position 3 Map Score: 19.6447 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 236 Number in noncoding regions = 314 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 TTCTGTGTTCCTGTAAATTCGGTGTTGTCGGA 1 278 0 CTGAAATTCG 0.968426 -23 ACCGCATTTCCTGAAAATTCACGCTGTATCTT 2 113 0 CTGAAATTCC 0.966765 -175 CACCACAATTCAGCAAATTGTGAACATCATCA 2 156 1 CAGAAATTGG 0.990867 -132 TCGTTACTGACAGGAAAATGGGCCATTGGCAA 2 205 0 CAGAAAATGG 0.983547 -83 TATGGTTTTGCAGGAAAATGCCCGAGATGTGA 3 126 1 CAGAAAATGC 0.983553 -159 CCGTGATTGCCAGTAAATCGACAACGGCGGCA 3 178 1 CAGAAATCGC 0.976071 -107 *** ****** * Masking position 6 Map Score: 4.24806 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 150 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 CGCTCGCGCGCATCCACGGCAATCAATGCC 1 223 0 CATCCACGGC 0.988535 -78 GAAAATGGGCCATTGGCAACCAGGGAAAGA 2 194 0 CATTGGCAAC 0.869514 -94 AAAGCGCCTGAATTCGCGACCTTCTCGTTA 2 231 0 AATTCGCGAC 0.905199 -57 CGGCATTAACAATCGGCCGCCCGACAATAC 3 22 0 AATCGGCCGC 0.951852 -263 GAACCAACTGCTTACGCGGCATTAACAATC 3 38 0 CTTACGCGGC 0.883377 -247 GATTTACTGGCAATCACGGCATTAAGTGGG 3 167 0 CAATCACGGC 0.938585 -118 AGTAAATCGACAACGGCGGCAACAGGCGAA 3 189 1 CAACGGCGGC 0.987768 -96 GCGAAAGGTTAATCGACAGCACGATTTTTA 3 214 1 AATCGACAGC 0.901902 -71 ********** Masking position 7 Map Score: 4.31401 Number of sites scoring better than the average of aligned sites = 3036 Number in coding regions = 2906 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 8 CAGCGTCGCATCAGGCATTGATTGCCGGAT 1 27 1 TCAGGCATTG 0.983157 -274 GTAGGCCGGATAAGGCACTTGTGCCGCATC 1 54 0 TAAGGCACTT 0.979754 -247 CAGCGTCGCATCAGGCATTGATTGCCGGAT 1 119 1 TCAGGCATTG 0.983157 -182 CGGATGCGCACAAGTCGCTTATCAGGCCTA 1 144 1 CAAGTCGCTT 0.634182 -157 CAGCGTCGCATCAGGCATTGATTGCCGTGG 1 210 1 TCAGGCATTG 0.983157 -91 GTAGGCCGGATAAGGCGCTCGCGCGCATCC 1 238 0 TAAGGCGCTC 0.963407 -63 AATCACGAGGTCAGGTTCTTACCTTAAATT 2 47 1 TCAGGTTCTT 0.807794 -241 GGTCGCGAATTCAGGCGCTTTTTAGACTGG 2 240 1 TCAGGCGCTT 0.993357 -48 ********** Masking position 3 Map Score: 8.72961 Number of sites scoring better than the average of aligned sites = 1826 Number in coding regions = 1675 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 9 GAAAAATCGACGTTTTTTACGTGGTTTTCC 2 83 0 CGTTTTTTAC 0.961858 -205 TAAAAAACGTCGATTTTTCAAGATACAGCG 2 94 1 CGATTTTTCA 0.948859 -194 CGAATTCAGGCGCTTTTTAGACTGGTCGTA 2 245 1 CGCTTTTTAG 0.953071 -43 GTCGGGCGGCCGATTGTTAATGCCGCGTAA 3 27 1 CGATTGTTAA 0.948866 -258 ATCGACAGCACGATTTTTACACTCATCTCG 3 225 1 CGATTTTTAC 0.984548 -60 ********** Masking position 5 Map Score: 1.6715 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 98 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 AGACGCGACAGCGTCGCATCAGGCATTGAT 1 19 1 GCGTCGCATC 0.988335 -282 AGACGCGACAGCGTCGCATCAGGCATTGAT 1 111 1 GCGTCGCATC 0.988335 -190 AGACGCGACAGCGTCGCATCAGGCATTGAT 1 202 1 GCGTCGCATC 0.988335 -99 CCTGATGTCGTCAACACGGCGAAATAGTAA 2 19 1 TCAACACGGC 0.732527 -269 AATGCGGTGAGCATCACATCACCACAATTC 2 137 1 GCATCACATC 0.993139 -151 ATTGTGAACATCATCACGTTCATCTTTCCC 2 172 1 TCATCACGTT 0.895395 -116 CTGCTGAATTTCATTACGACCAGTCTAAAA 2 259 0 TCATTACGAC 0.383476 -29 AAATTCAGCAGGATCACATT 2 278 1 GGATCACATT 0.701381 -10 TGGGTGATTTGCTTCACATCTCGGGCATTT 3 141 0 GCTTCACATC 0.962868 -144 GATTTACTGGCAATCACGGCATTAAGTGGG 3 167 0 CAATCACGGC 0.456307 -118 ATTTTTACACTCATCTCGTCGGAGATGTGA 3 237 1 TCATCTCGTC 0.906646 -48 ATTTTTCGTCGCGTCACATCTCCGACGAGA 3 250 0 GCGTCACATC 0.992667 -35 ********** Masking position 7 Map Score: 13.086 Number of sites scoring better than the average of aligned sites = 1908 Number in coding regions = 1635 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 11 ********** No masking Map Score: -1.44708e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: -1.44708e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: -1.44708e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0